Sat Oct 8 23:55:41 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 23:55:41 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2454 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6321023 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -13.29500 40.44600 ymin,ymax (A): -31.06600 25.25400 zmin,zma (A): -9.520000 33.47700 x,y,z range (A): 53.74100 56.32000 42.99700 scale (grids/A): 0.6321023 object centre (A): 13.57550 -2.906000 11.97850 number of atom coordinates read : 2454 total number of charged atoms : 2319 net assigned charge : 11.50002 assigned positive charge : 358.1191 centred at (gu) : 89.88919 91.10284 90.51733 assigned negative charge : -346.6199 centred at (gu) : 89.88145 91.10149 90.46004 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6695 nv = 96 ne = 84 npr = 48975 no. pairs analyzed = 48975 no. exposed pairs = 3206 no. arc points = 22990 no. surface atoms = 1078 nbur = 1376 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3505 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3534 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2341 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8070 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.6026181E-09 2.0125851E-08 midg,1,midg; midg,igrid,midg 1.0461408E-08 1.6870212E-08 1,midg,midg; igrid,midg,midg 1.2910505E-08 1.3591798E-08 gauss-seidel spectral radius is 0.9870316 estimated iterations to convergence 72 setup time was (sec) 0.4900000 now iterating at: 23:55:41 rms-change max change #iterations 0.1277158 18.69226 at 10iterations 1.2273807E-02 1.795517 at 20iterations 1.3620068E-03 0.2235031 at 30iterations 2.4750779E-04 4.6142578E-02 at 40iterations 7.6732162E-05 1.5771866E-02 at 50iterations finished qdiffx linear iterations at : 23:55:44 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 7.6732162E-05 1.5771866E-02 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 23:55:44 3.105u 0.136s 0:03.53 91.5% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 23:55:44 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2454 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.896307 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -13.29500 40.44600 ymin,ymax (A): -31.06600 25.25400 zmin,zma (A): -9.520000 33.47700 x,y,z range (A): 53.74100 56.32000 42.99700 scale (grids/A): 1.896307 object centre (A): 13.57550 -2.906000 11.97850 number of atom coordinates read : 2454 total number of charged atoms : 2319 net assigned charge : 11.50002 assigned positive charge : 358.1191 centred at (gu) : 89.66695 93.30814 91.55148 assigned negative charge : -346.6199 centred at (gu) : 89.64442 93.30444 91.37999 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 71995 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22990 grid for indexing accessible points = 1.400000 m= 25311 mr = 48439 m= 3969 mr = 18143 m= 232 mr = 2382 m= 1 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 262 time to turn everything in is 0.5000000 number of dielectric boundary points 32475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 18222 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6321023 object centre at (A) : 13.57550 -2.906000 11.97850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9026604E-03 2.1848446E-02 midg,1,midg; midg,igrid,midg 3.4955841E-02 3.0956749E-02 1,midg,midg; igrid,midg,midg 4.3425608E-02 4.7353633E-02 gauss-seidel spectral radius is 0.9986201 estimated iterations to convergence 213 setup time was (sec) 0.7600000 now iterating at: 23:55:45 rms-change max change #iterations 3.983069 171.2620 at 10iterations 1.850397 69.84171 at 20iterations 0.8630559 32.75633 at 30iterations 0.4018029 14.50611 at 40iterations 0.1872387 5.815830 at 50iterations 8.7186411E-02 2.952932 at 60iterations 4.0541012E-02 1.225847 at 70iterations 1.8975643E-02 0.6053410 at 80iterations 8.8961003E-03 0.2948685 at 90iterations 4.1756462E-03 0.1346633 at 100iterations 1.9895926E-03 6.1813354E-02 at 110iterations 9.6703600E-04 3.2707214E-02 at 120iterations finished qdiffx linear iterations at : 23:55:51 total time elapsed so far: 6.720000 # loops : 120 mean,max change (kT/e) : 9.6703600E-04 3.2707214E-02 energy calculations done at 6.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.900000 DelPhi exited at 23:55:52 6.903u 0.158s 0:07.33 96.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 23:55:52 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2454 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.844460 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -13.29500 40.44600 ymin,ymax (A): -31.06600 25.25400 zmin,zma (A): -9.520000 33.47700 x,y,z range (A): 53.74100 56.32000 42.99700 scale (grids/A): 2.844460 object centre (A): 13.57550 -2.906000 11.97850 number of atom coordinates read : 2454 total number of charged atoms : 2319 net assigned charge : 11.50002 assigned positive charge : 358.1191 centred at (gu) : 89.50027 94.96206 92.32698 assigned negative charge : -346.6199 centred at (gu) : 89.46652 94.95663 92.07005 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 166266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22990 grid for indexing accessible points = 1.400000 m= 81892 mr = 117661 m= 29281 mr = 65507 m= 7012 mr = 23154 m= 996 mr = 5194 m= 54 mr = 619 m= 0 mr = 24 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 996 time to turn everything in is 1.250000 number of dielectric boundary points 73342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 18550 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.896307 object centre at (A) : 13.57550 -2.906000 11.97850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4669865E-02 0.2178162 midg,1,midg; midg,igrid,midg 0.5029118 0.3652478 1,midg,midg; igrid,midg,midg 0.4086280 0.5212017 gauss-seidel spectral radius is 0.9992593 estimated iterations to convergence 290 setup time was (sec) 1.530000 now iterating at: 23:55:53 rms-change max change #iterations 9.465689 328.2419 at 10iterations 5.586017 134.0905 at 20iterations 3.263708 69.92015 at 30iterations 1.903342 40.74463 at 40iterations 1.108243 22.52296 at 50iterations 0.6426092 13.02548 at 60iterations 0.3722178 7.653711 at 70iterations 0.2150466 4.265134 at 80iterations 0.1244449 2.446248 at 90iterations 7.1692608E-02 1.420799 at 100iterations 4.1445184E-02 0.8014565 at 110iterations 2.3939554E-02 0.4490128 at 120iterations 1.3852889E-02 0.2632761 at 130iterations 8.0368631E-03 0.1639233 at 140iterations 4.7114179E-03 9.6345901E-02 at 150iterations 2.8117192E-03 6.0184479E-02 at 160iterations 1.7238023E-03 4.3629646E-02 at 170iterations 1.1070906E-03 2.8544426E-02 at 180iterations finished qdiffx linear iterations at : 23:56:03 total time elapsed so far: 11.26000 # loops : 180 mean,max change (kT/e) : 1.1070906E-03 2.8544426E-02 energy calculations done at 11.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.42000 DelPhi exited at 23:56:04 11.423u 0.158s 0:11.95 96.8% 0+0k 0+0io 0pf+0w